took vep_fields into CONSTANT for use in both 454 data & vcf data; put vcf data into %exon_data_ref for use in post-vep processing (as used in 454 data-files); adapted vep_location / ref_location comparison to handle insertions where end position < start position; moved counts & errors into separate 'data' hashref in results; completed adaptation of VEP for vcf data-files

adapted NGS::VEP to accept vcf files - imported vcf-to-vep.pl script code

new vcf analysis section; moved ChartMaker to NGS::ChartMaker

moved ngs.pl startup script stderr & stdout to go to NGS/logs/deployment.log; made path to debug.txt explicit in NGS::VEP

needed FindBin in app.pl after update to D2 v0.09; bootstrap 3.0.0 spacelabs theme

patched VEP::_get_hmds_refs to return error if col header doesn't look like lab number; 015_data.t to test

fixed refseq selection function - required separate cache dir & use of --dir option

added transcription db = refseq option; fix for FLT3-ITD 1 variant; tests for invalid variant format

added errors & alerts display to results output; checks all exon names in src data are in vep input data; updated test scripts with results output format

renamed vep orphans to non-CDS regions; added new ref entry to sqlite db; results page displays input src filename

added 2 cols to VEP table (position in CDS and position in protein; added 12 new exons in ref table

bugfix to _prediction_and_score() - needed to skip undef vars; colour-coded results if deleterious or damaging; truncated long (>30 char) variation results; re-ordered results cols for clarity

escaped spaces in tt a name var; changed production env flag to deployment

added specific vep row counter to sample_data results for use in both sample match and sample no-match displays

discontinued NGS::MooX::Types; put proper result counters in using VEP result_counter attribute